One issue I ran into was a change in how Environment Naming Context (ENC) java:comp/env is handeled. In JBoss-4.2.3.GA an init-Thread created by an ENC aware MainDeployer-Thread would also have ENC with JNDI lookup on comp/env succeeding.

In JBoss-6.0.0.Final the same init-Thread would not have an ENC it seems

Tried to switch to AS managed Threading, tried AS6 introduced Thread Pool Configuration as described in: